User:Max Lein/Sandbox

About this Structure
The PDB 1gpa contains 4 chains of the 'A' form of glycogen phosphorylase. Each subunit contains a phosphate group bound to Ser14, sulfate groups bound to two effector sites (sulfate acts as a mimic of phosphate groups), and the cofactor pyridoxal-5'-phosphate bound to K681. See the links section at the end of this page for links to more structural information on glycogen phosphorylase.

Reaction
Glycogen phosphorylase (GP) catalyzes the degradation of the reducing end of glycogen into glucose-1-phosphate. It employs a cofactor called pyridoxal-5’ –phosphate, that is located in the active site and bound to a K681 residue with a Schiff base linkage. PLP shuttles the phosphate group onto the substrate.

History
This protein comes from the muscle tissue of Oryctolagus cuniculus. There is an isozyme from liver tissue that is regulated by glucagon instead of epinephrine, with a different gene that encodes it and different regulation properties.

Glycogen phosphorylase was the first phosphorylase enzyme to be discovered, and the first example of regulation via covalent modification.

In the 1930s, the first work done by Carl and Gerty Cori. They proved that the enzyme exists in 'A' and 'B' forms, and they showed that the reverse reaction produced glycogen. They won the Nobel Prize in 1947 along with Bernardo Housay of Argentina for their work on carbohydrate metabolism. This was also the first example of a polymerizing enzyme, inspiring others to look for other polymerizing enzymes.

Subsequently, Earl Sutherland found that the 'B' form predominates in resting muscle and epinephrine triggers activation to form 'A'. Since then, many groups have worked on this enzyme, both to understand its mechanism and to discover drug targets. Crystal structures have been obtained for the protein in the 'A' and 'B' form, in the presence of natural substrates, inhibitors, and transition state analogs. Please see the end of this article for links to crystallographic information.

Activity and Regulation of GP
In its active form, GP is a dimer of two identical subunits. The subunits make interactions that stabilize the final structure.

Each Sub-unit contains 5 potential effector sites: 1. Ser14 phosphate-recognition site. 2. AMP activation / Glc-6-P inhibition site. 3. Catalytic site that binds glycogen, Glc-1-P 4. Inhibitor site, 12Å from catalytic site, binds caffeine and related compounds. 5. Glycogen storage site.

There are two forms of the enzyme, designated as 'A' and 'B', that are controlled hormonally. The 'B' form is converted into the 'A' form by phosphorylase kinase, which catalyzes the addition of phosphate from ATP to Ser14 near the N-terminus. This represents the final step in a signal transduction cascade in response to the hormone epinephrine, associated with the 'fight-or-flight' response and causing an increase in available energy to the organism as a whole. The N-terminus contains a high percentage of basic residues, which interact favorably with a pocket of acidic residues (Asp109, Glu110, Glu120, Glu501, Glu505 and Glu509) in the 'B' form. Once Ser14 is phosphorylated, the N-terminus is forced ~50Å away from the acidic residues, settling into a region with R69 and R45' (prime denotes a residue from the adjacent subunit). In summary, the conformatino change causes an ordering of the N-terminal chain and a disordering of residues at the C-terminal. Once disordered, the C-terminal residues are no longer able to block substrate entry into the active site. The enzyme phosphatase is able to remove the phosphate and return GP to form 'B'.

In addition, the 'A' and 'B' forms can be regulated futher by small molecules in the cell. This allows individual cells to ignore the hormonal signal if they already have enough available energy (at high concentrations of glucose derivatives or ATP, designated as the 'T' state for low substrate affinity), or activate GP without a hormonal signal when energy for the individual cell is needed (high concentrations of AMP, designated as the 'R' state for high substrate affinity).

Links
1GPA is a Single protein structure of sequence from Oryctolagus cuniculus. Additional information on 1GPA is available in a page on Glycogen Phosphorylase at the RCSB PDB Molecule of the Month. Full crystallographic information is available from OCA.